Libraries Used

• Our analysis for this presenation would not have been possible without these libaries:

library(survival)
library(KMsurv)
library(ggplot2)
library(ggpubr)
library(survminer)
library(plotly)
library(muhaz)
library(ggthemes)
library(plyr)

Loading in Data

data(std)
std

## [1] FALSE

Exploratory Data Analysis

Take a look at correlation between symptoms and different infection types.

Is it more common for one type of infection based on type of sex (oral/anal).

Kaplan-Meier Curves

## Call:
## survdiff(formula = surv_object ~ iinfct, data = std)
## 
##                    N Observed Expected (O-E)^2/E (O-E)^2/V
## iinfct=gonorrhea 140       73     54.5   6.28042   7.50617
## iinfct=chlamydia 396      135    153.0   2.12201   3.81136
## iinfct=both      341      139    139.5   0.00166   0.00278
## 
##  Chisq= 8.5  on 2 degrees of freedom, p= 0.01

Cumulative Hazards and CLogLog

Schoenfield Residuals for Initial Infection

• P-value here is large, so we do not have a violation of proportional hazards.

## Call:
## coxph(formula = surv_object ~ iinfct, data = std)
## 
##   n= 877, number of events= 347 
## 
##                    coef exp(coef) se(coef)      z Pr(>|z|)   
## iinfctchlamydia -0.4202    0.6569   0.1457 -2.884  0.00393 **
## iinfctboth      -0.2980    0.7423   0.1450 -2.055  0.03984 * 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
##                 exp(coef) exp(-coef) lower .95 upper .95
## iinfctchlamydia    0.6569      1.522    0.4937    0.8741
## iinfctboth         0.7423      1.347    0.5587    0.9863
## 
## Concordance= 0.524  (se = 0.016 )
## Likelihood ratio test= 7.93  on 2 df,   p=0.02
## Wald test            = 8.37  on 2 df,   p=0.02
## Score (logrank) test = 8.46  on 2 df,   p=0.01

Building a full model

cox1 <-
  coxph(
    surv_object ~ iinfct + marital + race + os12m + os30d + rs12m + rs30d + abdpain + discharge + dysuria + condom + itch + lesion + rash + lymph + vagina + dchexam + abnode + age + yschool + npartner,
    data = std
  )

## Call:
## coxph(formula = surv_object ~ iinfct + marital + race + os12m + 
##     os30d + rs12m + rs30d + abdpain + discharge + dysuria + condom + 
##     itch + lesion + rash + lymph + vagina + dchexam + abnode + 
##     age + yschool + npartner, data = std)
## 
##   n= 877, number of events= 347 
## 
##                      coef exp(coef)  se(coef)      z Pr(>|z|)   
## iinfctchlamydia -0.334628  0.715604  0.149647 -2.236  0.02534 * 
## iinfctboth      -0.267515  0.765279  0.149987 -1.784  0.07449 . 
## maritalMarried   0.055058  1.056602  0.431303  0.128  0.89842   
## maritalSingle    0.408097  1.503953  0.295341  1.382  0.16704   
## raceWhite       -0.111462  0.894526  0.141327 -0.789  0.43030   
## os12m1          -0.206151  0.813711  0.212028 -0.972  0.33091   
## os30d1          -0.339983  0.711783  0.238657 -1.425  0.15428   
## rs12m1           0.033955  1.034538  0.445166  0.076  0.93920   
## rs30d1          -0.194771  0.823023  0.565199 -0.345  0.73039   
## abdpain1         0.229308  1.257729  0.156236  1.468  0.14219   
## discharge1       0.114691  1.121527  0.114283  1.004  0.31559   
## dysuria1         0.164089  1.178320  0.155157  1.058  0.29025   
## condomsometime  -0.064082  0.937928  0.239642 -0.267  0.78916   
## condomnever     -0.321968  0.724721  0.247790 -1.299  0.19382   
## itch1           -0.147451  0.862905  0.154774 -0.953  0.34075   
## lesion1         -0.183670  0.832210  0.333523 -0.551  0.58184   
## rash1            0.008298  1.008333  0.392928  0.021  0.98315   
## lymph1          -0.030840  0.969631  0.547496 -0.056  0.95508   
## vagina1          0.351398  1.421053  0.174868  2.010  0.04448 * 
## dchexam1        -0.463338  0.629180  0.230020 -2.014  0.04397 * 
## abnode1          0.170712  1.186149  0.433788  0.394  0.69392   
## age              0.008096  1.008129  0.013913  0.582  0.56066   
## yschool         -0.128072  0.879790  0.039366 -3.253  0.00114 **
## npartner         0.076670  1.079686  0.053888  1.423  0.15480   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
##                 exp(coef) exp(-coef) lower .95 upper .95
## iinfctchlamydia    0.7156     1.3974    0.5337    0.9595
## iinfctboth         0.7653     1.3067    0.5704    1.0268
## maritalMarried     1.0566     0.9464    0.4537    2.4606
## maritalSingle      1.5040     0.6649    0.8430    2.6830
## raceWhite          0.8945     1.1179    0.6781    1.1800
## os12m1             0.8137     1.2289    0.5370    1.2330
## os30d1             0.7118     1.4049    0.4459    1.1363
## rs12m1             1.0345     0.9666    0.4323    2.4756
## rs30d1             0.8230     1.2150    0.2718    2.4918
## abdpain1           1.2577     0.7951    0.9260    1.7083
## discharge1         1.1215     0.8916    0.8965    1.4031
## dysuria1           1.1783     0.8487    0.8693    1.5971
## condomsometime     0.9379     1.0662    0.5864    1.5002
## condomnever        0.7247     1.3798    0.4459    1.1778
## itch1              0.8629     1.1589    0.6371    1.1687
## lesion1            0.8322     1.2016    0.4328    1.6000
## rash1              1.0083     0.9917    0.4668    2.1780
## lymph1             0.9696     1.0313    0.3316    2.8355
## vagina1            1.4211     0.7037    1.0087    2.0020
## dchexam1           0.6292     1.5894    0.4008    0.9876
## abnode1            1.1861     0.8431    0.5069    2.7758
## age                1.0081     0.9919    0.9810    1.0360
## yschool            0.8798     1.1366    0.8145    0.9504
## npartner           1.0797     0.9262    0.9715    1.2000
## 
## Concordance= 0.635  (se = 0.016 )
## Likelihood ratio test= 73.37  on 24 df,   p=7e-07
## Wald test            = 69.89  on 24 df,   p=2e-06
## Score (logrank) test = 71.71  on 24 df,   p=1e-06